Part Of Clade Research Articles

TWO NEW SPECIES OF STILLABOTHRIUM (CESTODA: RHINEBOTHRIIDEA) FROM STINGRAYS FROM NORTHERN AUSTRALIA AND ONE NEW COMBINATION.

A study of cestode specimens that were collected during survey work on elasmobranchs collected from Taiwan and Northern Territory, Australia, revealed the presence of 1 new combination into the genus Stillabothrium (Rhinebothriidea: Escherbothriidae) and 2 new species of the genus. Phyllobothrium biacetabulatum, collected from Rhinobatos schlegelii, is transferred to Stillabothrium and its description is emended, as is the diagnosis for the genus Stillabothrium and the family Escherbothriidae. Stillabothrium biacetabulatum n. comb. differs from existing species of the genus in that the face of its bothridia is laced with a network of longitudinal and horizontal muscle fibers that do not contribute to the formation of septa. Stillabothrium lunae n. sp. is described from Himantura leoparda and differs from existing species of the genus in that its bothridium possesses an anterior field of 7-8 loculi that are wider than long. Stillabothrium mariae n. sp. is described from Maculabatis astra. This species differs from all species of Stillabothrium except Stillabothrium campbelli in possessing 10-12 horizontally oriented bothridial loculi. Stillabothrium mariae n. sp. differs from S. campbelli in having longer bothridia and from all other species of Stillabothrium in that it lacks, rather than possesses, conspicuous septa and loculi that are longer than wide in the posterior region of its bothridia. Bayesian and parsimony-bootstrap analysis of 28S rDNA revealed S. biacetabulatum n. comb., S. lunae n. sp., and S. mariae n. sp. to be part of Clade 1 of Stillabothrium, with S. biacetabulatum n. comb. being the sister species to S. mariae n. sp. Stillabothrium lunae n. sp. was found to be the sister species to Stillabothrium borneoense.

An outbreak of Clostridium difficile infections due to new PCR ribotype 826: epidemiologic and microbiologic analyses

ObjectivesTo investigate an unusual outbreak of five patients with a total of eight episodes of a Clostridium difficile infection on a gastrointestinal surgical ward of a Dutch tertiary-care, university-affiliated hospital. MethodsClinical case investigations and laboratory analyses were performed. Laboratory analyses included PCR ribotyping, multiple-locus variable-number tandem repeat analysis typing, toxin typing, antimicrobial susceptibility testing and whole genome sequencing. ResultsThe outbreak was associated with recurrent and severe disease in two of five patients. All episodes were due to a unique ribotype that was not recognized in the collection of an international network of reference laboratories and was assigned PCR ribotype 826. PCR ribotype 826 is a toxin A–, toxin B– and binary toxin–positive ribotype which according to molecular typing belongs to clade 5 and resembles the so-called hypervirulent ribotype 078. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this newly identified ribotype remained unclear. ConclusionsThis newly identified C. difficile PCR ribotype 826 is part of clade 5 and might also have increased virulence. The recognition of this outbreak highlights the need for ongoing C. difficile infection surveillance to monitor new circulating ribotypes with assumed increased virulence.

Influence of host and geographic locale on the distribution of Colletotrichum cereale lineages.

Colletotrichum cereale is an ascomycete inhabitant of cool-season Pooideae grasses. The fungus has increased in frequency over the past decade as a destructive pathogen of Poa annua and Agrostis stolonifera turfgrass. Colletotrichum cereale exists as two lineages, designated clades A and B, but little is known about the distribution of these clades in natural environments, or what role these subdivisions may play in the trajectory of disease outbreaks. In this study, our objective was to determine the frequency of C. cereale clades A and B. To rapidly discriminate between the two C. cereale clades, a real-time PCR assay was developed based on the Apn2 gene. A collection of 700 C. cereale pathogens and endophytes from twenty Pooideae grass genera were genotyped. 87% of the collection was identifed as part of clade A, 11.7% as part of clade B, and 1.3% was a mixture. Colletotrichum cereale from turfgrass hosts in North America were most commonly members of clade A (78%). The overabundance of clade A in turfgrass isolates was directly attributable to the dominance of this lineage from southern sampling sites, irrespective of host. In contrast, 111 C. cereale turfgrass isolates collected from northern sampling sites were evenly distributed between clades A and B. Only 28% of C. cereale from A. stolonifera at northern sampling sites were part of clade A. These data show that environmental factors such as geographic location and host identity likely played a role in the distribution of the major C. cereale clades in North American turfgrass.

Quaternary ostracodes and molluscs from the Rukwa Basin (Tanzania) and their evolutionary and paleobiogeographic implications

Much of the spectacular biodiversity of the African Great Lakes is endemic to single lake basins so that the margins of these basins or their lakes coincide with biogeographic boundaries. Longstanding debate surrounds the evolution of these endemic species, the stability of bioprovinces, and the exchange of faunas between them over geologic time as the rift developed. Because these debates are currently unsettled, we are uncertain of how much existing distribution patterns are determined by modern hydrological barriers versus reflecting past history. This study reports on late Quaternary fossils from the Rukwa Basin and integrates geological and paleoecological data to explore faunal exchange between freshwater bioprovinces, in particular with Lake Tanganyika. Lake Rukwa's water level showed large fluctuations over the last 25ky, and for most of this period the lake contained large habitat diversity, with different species assemblages and taphonomic controls along its northern and southern shores. Comparison of fossil and modern invertebrate assemblages suggests faunal persistence through the Last Glacial Maximum, but with an extirpation event that occurred in the last 5ky. Some of the molluscs and ostracodes studied here are closely related to taxa (or part of clades) that are currently endemic to Lake Tanganyika, but others testify to wider and perhaps older faunal exchanges between the Rukwa bioprovince and those of Lake Malawi and the Upper Congo (in particular Lake Mweru). The Rukwa Basin has a long history of rifting and lacustrine conditions and, at least temporarily, its ecosystems appear to have functioned as satellites to Lake Tanganyika in which intralacustrine speciation occurred. Paleontological studies of the Rukwa faunas are particularly relevant because of the basin's important role in the late Cenozoic biogeography of tropical Africa, and because many of the molecular traces potentially revealing this history would have been erased in the late Holocene extirpation.

Intraregional variation among Alexandrium catenella (Dinophyceae) strains from southern Chile: Morphological, toxicological and genetic diversity

Morphological, toxicological and phylogenetic analyses, using the partial LSU gene and internal spacer (ITS) regions of the rDNA gene, were combined to evaluate the intraregional diversity of Alexandrium catenella occurring along the southern coast of Chile. Twenty-two strains isolated from different localities along the wide area of distribution of the species (from 42°S to 55°S) were examined by these three approaches. Morphologically, although the strains showed diagnostic characters according to the species definition, variations in these traits within and between strains were also observed. The absence of an apical or posterior attachment pore, for instance, was observed mainly in old isolates. Indirect connection between the apical and 1′ plates, traits normally seen in other species of the same genus, was also noted in some strains. However, the lack of a ventral pore on the 1′ plate was one of the most distinctive characteristics present in all the Chilean strains. Toxicologically, the Chilean strains were characterized by the dominance of N-sulfocarbamate (C1,2) and gonyautoxins (GTX1–4), but also by the scarcity or absence of saxitoxin. Considering the dominance of these toxins in each strain, at least two distinctive toxin patterns were distinguished. Through rDNA sequence analysis, the Chilean strains were segregated as part of Clade I (North American) of the Alexandrium tamarense species complex. Nevertheless, significant genetic diversity was also observed among the Chilean strains, especially using ITS sequences. Through these three approaches, Chilean strains of A. catenella showed significant intraregional variability, which is appropriate for a native species. However, the distribution of its genetic diversity seems to be inconsistent with the apparent northward expansion observed along the west coast of South America.

AHSP Is a Quantitative Trait Gene That Modifies the Phenotype of β Thalassemia.

Alpha hemoglobin stabilizing protein (AHSP) was identified in a screen for genes that are activated by the erythroid transcription factor, GATA-1. Studies have shown that:AHSP binds specifically to the α chain of hemoglobin (Hb) but not to β Hb or Hb A;AHSP knock-out mice demonstrated pathological features similar to β thalassemia; andloss of AHSP exacerbates severity of disease in β thalassemia mice.The evidence suggests that AHSP acts as a chaperone for free α Hb and that altered AHSP expression levels could modify the severity of β thalassemia in humans.To assess variation of AHSP expression, mRNA levels were measured in peripheral blood reticulocytes of 103 healthy individuals by quantitative real-time RT-PCR. The sample was approximately 90% (91/103) female with an average age of 52 years (SD=0.14, min=18, max=76). AHSP expression relative to GAPDH, varied up to 3-fold, and did not correlate with age or sex. A systematic survey of the genomic region encompassing the AHSP locus revealed 8 sequence variants of which six were common - five single nucleotide polymorphisms (SNPs), and one homopolymer (Tn) at position 160 bp upstream of exon 1. Four variants (c.-69–237A, c.-69–160 T18, c.-4–27G, and c. 337T) showed strong association with AHSP expression and had nearly equal frequencies. The four variants are in near complete linkage disequilibrium with the minor alleles in coupling. The haplotype consisting of the four minor alleles termed clade B, was associated with relatively lower expression of AHSP. Relative expression of AHSP and AHSP/α globin ratio were both significantly higher (p<0.001) in homozygotes for clade A haplotypes compared to heterozygotes. A potential functional role of one of the variable sites, a T-homopolymer (the T18 variant being part of clade A) in the promoter was investigated in-vitro using luciferase reporter assays in K562 cells. Luciferase activity was 1.30±0.08 times higher in the T18 promoter compared to T14, consistent with genetic studies. We investigated if a shorter homopolymer could have an adverse effect on β thalassemia. Nine patients with thalassemia intermedia and a genotypic combination of heterozygous β thalassemia and 5 α globin genes (aaa/aa) were studied. Based on the allele frequencies in the healthy population, 6–7 of the 9 patients are expected to be homozygous for T18 but only two were observed. In contrast, while 2–3 patients are expected to be heterozygous for the shorter homopolymer, 3 patients were homozygous and 4 heterozygous.In conclusion, AHSP gene expression is variable, with cis control accounting for some of its variance. The subtle altered expression might precipitate a phenotype of thalassemia intermedia in β thalassemia heterozygotes with α globin overload.

Patterns of evolution in Australian Mimulus and related genera (Phrymaceae~Scrophulariaceae): a molecular phylogeny using chloroplast and nuclear sequence data

The aim of this work was to develop rigorous phylogenetic hypotheses for the mostly Australian species of Mimulus, Glossostigma, Peplidium, Microcarpaea and Elacholoma (Phrymaceae sensu Beardsley and Olmstead 2002), and to use the phylogeny to explore morphological patterns of evolution. Chloroplast trnL/F and nuclear ribosomal internal and external transcribed spacer sequence data were used to analyse phylogenetic relationships. The results of these analyses confirmed the following conclusions proposed in previous morphological analyses: (1) Glossostigma and Peplidium are supported as monophyletic groups, although support is weak for Peplidium; (2) Australian endemic Elacholoma, in the past of uncertain family placement, is embedded within the same clade as the former two genera despite its unique pair of terete stigmatic lobes; (3) a relatively recent dispersal event from Australia to Iraq and the Middle East for P. maritimum is inferred; (4) a reduction in stamen number from four to two has evolved independently several times in Glossostigma, Peplidium, Microcarpaea and Elacholoma; (5) a switch to an obligately autogamous breeding system has evolved several times independently in the group. New findings include the following: (1) Glossostigma, Peplidium, Microcarpaea and Elacholoma are derived from within Mimulus; (2) Mimulus prostratus is part of a clade that contains Elacholoma and Glossostigma, and this clade is not a part of the same clades as other Mimulus species in Australia; (3) there is some support for Microcarpaea being sister to a clade including Elacholoma, Mimulus prostratus, Glossostigma and Peplidium. The discovery that four mostly Australian genera are derived from within the mostly western North American genus Mimulus has important implications for generic assignments. Phylogenetic interpretations of additional morphological character transformations are discussed.

A Molecular Perspective on the Systematics and Evolution of the GenusArvicanthis(Rodentia, Muridae): Inferences from Complete CytochromebGene Sequences

Systematics of the genusArvicanthis,the African unstriped grass rat, are somewhat controversial. Most recent taxonomic revisions list five to six species but the definition of some of these (Arvicanthis dembeensis, Arvicanthis nairobae,andArvicanthis niloticus) is uncertain. The complete mitochondrial cytochromebgene (1140 bp) was sequenced for 20 specimens from throughout the range of the genus to determine the intrageneric genetic structure, construct a molecular phylogeny, and evaluate classical taxonomies. Neighbor-joining and maximum parsimony analyses yielded identical phylogenetic trees that identify two major lineages: the first one (1) is composed of specimens usually referred toA. niloticusbut representing several distinct species, and the other (2) is a complex including “true”A. niloticusfrom Egypt and northern West Africa as well asArvicanthis abyssinicus, Arvicanthis dembeensis,andArvicanthis somalicus.An analysis on a 357-bp fragment of the cytochromebincluding published data onA. nairobaeindicates that this taxon is part of clade (1). Calibration of the number of 3rd position transversion changes with the murid fossil record suggests that clades (1) and (2) diverged approximately 5 Myr ago.Arvicanthis niloticusas currently recognized is a paraphyletic association and this name should be restricted to the Egyptian and northern West African sample. We also suggest referring toA. dembeensisasA. niloticus,as our cytochromebdata do not support its recognition as a distinct species. Clade (1) is subdivided in three lineages, geographically corresponding to southern West, Central, and East Africa. The high genetic divergence detected between the Central African lineage and the other two lineages suggests that they probably represent separate species. Clade (2) experienced rapid cladogenetic events during the late Pliocene, with theA. somalicuslineage being the first to emerge, followed by the ancestor ofA. abyssinicusandA. blicki.This period was characterized by significant climatic and environmental changes, such as the extension of open habitats, which might have provided a stimulus for speciation in this savanna-dwelling genus. Confrontation of our molecular results with chromosomal data shows a high degree of congruence between the two datasets.